Data processing methods and data acquisition for samples larger than the field of view in parallel-beam tomography.

Parallel-beam tomography systems at synchrotron facilities have limited field of view (FOV) determined by the available beam size and detector system coverage. Scanning the full size of samples bigger than the FOV requires various data acquisition schemes such as grid scan, 360-degree scan with offset center-of-rotation (COR), helical scan, or combinations of these schemes. Though straightforward to implement, these scanning techniques have not often been used due to the lack of software and methods to process such types of data in an easy and automated fashion. The ease of use and automation is critical at synchrotron facilities where using visual inspection in data processing steps such as image stitching, COR determination, or helical data conversion is impractical due to the large size of datasets. Here, we provide methods and their implementations in a Python package, named Algotom, for not only processing such data types but also with the highest quality possible. The efficiency and ease of use of these tools can help to extend applications of parallel-beam tomography systems.

X-ray phase-contrast imaging with engineered porous materials over 50†keV.

X-ray phase-contrast imaging can substantially enhance image contrast for weakly absorbing samples. The fabrication of dedicated optics remains a major barrier, especially in high-energy regions (i.e. over 50 keV). Here, the authors perform X-ray phase-contrast imaging by using engineered porous materials as random absorption masks, which provides an alternative solution to extend X-ray phase-contrast imaging into previously challenging higher energy regions. The authors have measured various samples to demonstrate the feasibility of the proposed engineering materials. This technique could potentially be useful for studying samples across a wide range of applications and disciplines.

Superior techniques for eliminating ring artifacts in X-ray micro-tomography.

Synchrotron-based X-ray micro-tomography systems often suffer severe ring artifacts in reconstructed images. In sinograms the artifacts appear as straight lines or stripe artifacts. These artifacts are caused by the irregular response of a detecting system giving rise to a variety of observed types of stripes: full stripes, partial stripes, fluctuating stripes, and unresponsive stripes. The use of pre-processing techniques such as distortion correction or phase retrieval blurs and enlarges these stripes. It is impossible for a single approach to remove all types of stripe artifacts. Here, we propose three techniques for tackling all of them. The proposed techniques are easy to implement; do not generate extra stripe artifacts and void-center artifacts; and give superior quality on challenging data sets and in comparison with other techniques. Implementations in Python and a challenging data set are available for download.

A novel molten-salt electrochemical cell for investigating the reduction of uranium dioxide to uranium metal by lithium using in situ synchrotron radiation.

A novel electrochemical cell has been designed and built to allow for in situ energy-dispersive X-ray diffraction measurements to be made during reduction of UO2 to U metal in LiCl-KCl at 500°C. The electrochemical cell contains a recessed well at the bottom of the cell into which the working electrode sits, reducing the beam path for the X-rays through the molten-salt and maximizing the signal-to-noise ratio from the sample. Lithium metal was electrodeposited onto the UO2 working electrode by exposing the working electrode to more negative potentials than the Li deposition potential of the LiCl-KCl eutectic electrolyte. The Li metal acts as a reducing agent for the chemical reduction of UO2 to U, which appears to proceed to completion. All phases were fitted using Le Bail refinement. The cell is expected to be widely applicable to many studies involving molten-salt systems.

Almost a spider: a 305-million-year-old fossil arachnid and spider origins.

Spiders are an important animal group, with a long history. Details of their origins remain limited, with little knowledge of their stem group, and no insights into the sequence of character acquisition during spider evolution. We describe a new fossil arachnid, Idmonarachne brasierigen. et sp. nov. from the Late Carboniferous (Stephanian,ca 305-299 Ma) of Montceau-les-Mines, France. It is three-dimensionally preserved within a siderite concretion, allowing both laboratory- and synchrotron-based phase-contrast computed tomography reconstruction. The latter is a first for siderite-hosted fossils and has allowed us to investigate fine anatomical details. Although distinctly spider-like in habitus, this remarkable fossil lacks a key diagnostic character of Araneae: spinnerets on the underside of the opisthosoma. It also lacks a flagelliform telson found in the recently recognized, spider-related, Devonian-Permian Uraraneida. Cladistic analysis resolves our new fossil as sister group to the spiders: the spider stem-group comprises the uraraneids and I. brasieri While we are unable to demonstrate the presence of spigots in this fossil, the recovered phylogeny suggests the earliest character to evolve on the spider stem-group is the secretion of silk. This would have been followed by the loss of a flagelliform telson, and then the ability to spin silk using spinnerets. This last innovation defines the true spiders, significantly post-dates the origins of silk, and may be a key to the group's success. The Montceau-les-Mines locality has previously yielded a mesothele spider (with spinnerets). Evidently, Late Palaeozoic spiders lived alongside Palaeozoic arachnid grades which approached the spider condition, but did not express the full suite of crown-group autapomorphies.

I12: the Joint Engineering, Environment and Processing (JEEP) beamline at Diamond Light Source.

I12 is the Joint Engineering, Environmental and Processing (JEEP) beamline, constructed during Phase II of the Diamond Light Source. I12 is located on a short (5 m) straight section of the Diamond storage ring and uses a 4.2 T superconducting wiggler to provide polychromatic and monochromatic X-rays in the energy range 50-150 keV. The beam energy enables good penetration through large or dense samples, combined with a large beam size (1 mrad horizontally × 0.3 mrad vertically). The beam characteristics permit the study of materials and processes inside environmental chambers without unacceptable attenuation of the beam and without the need to use sample sizes which are atypically small for the process under study. X-ray techniques available to users are radiography, tomography, energy-dispersive diffraction, monochromatic and white-beam two-dimensional diffraction/scattering and small-angle X-ray scattering. Since commencing operations in November 2009, I12 has established a broad user community in materials science and processing, chemical processing, biomedical engineering, civil engineering, environmental science, palaeontology and physics.

Radial lens distortion correction with sub-pixel accuracy for X-ray micro-tomography.

Distortion correction or camera calibration for an imaging system which is highly configurable and requires frequent disassembly for maintenance or replacement of parts needs a speedy method for recalibration. Here we present direct techniques for calculating distortion parameters of a non-linear model based on the correct determination of the center of distortion. These techniques are fast, very easy to implement, and accurate at sub-pixel level. The implementation at the X-ray tomography system of the I12 beamline, Diamond Light Source, which strictly requires sub-pixel accuracy, shows excellent performance in the calibration image and in the reconstructed images.

A high-throughput system for high-quality tomographic reconstruction of large datasets at Diamond Light Source.

Tomographic datasets collected at synchrotrons are becoming very large and complex, and, therefore, need to be managed efficiently. Raw images may have high pixel counts, and each pixel can be multidimensional and associated with additional data such as those derived from spectroscopy. In time-resolved studies, hundreds of tomographic datasets can be collected in sequence, yielding terabytes of data. Users of tomographic beamlines are drawn from various scientific disciplines, and many are keen to use tomographic reconstruction software that does not require a deep understanding of reconstruction principles. We have developed Savu, a reconstruction pipeline that enables users to rapidly reconstruct data to consistently create high-quality results. Savu is designed to work in an 'orthogonal' fashion, meaning that data can be converted between projection and sinogram space throughout the processing workflow as required. The Savu pipeline is modular and allows processing strategies to be optimized for users' purposes. In addition to the reconstruction algorithms themselves, it can include modules for identification of experimental problems, artefact correction, general image processing and data quality assessment. Savu is open source, open licensed and 'facility-independent': it can run on standard cluster infrastructure at any institution.

Morquio A syndrome-associated mutations: a review of alterations in the GALNS gene and a new locus-specific database.

Morquio A syndrome (mucopolysaccharidosis IVA) is an autosomal recessive disorder that results from deficient activity of the enzyme N-acetylgalactosamine-6-sulfatase (GALNS) due to alterations in the GALNS gene, which causes major skeletal and connective tissue abnormalities and effects on multiple organ systems. The GALNS alterations associated with Morquio A are numerous and heterogeneous, and new alterations are continuously identified. To aid detection and interpretation of GALNS alterations, from previously published research, we provide a comprehensive and up-to-date listing of 277 unique GALNS alterations associated with Morquio A identified from 1,091 published GALNS alleles. In agreement with previous findings, most reported GALNS alterations are missense changes and even the most frequent alterations are relatively uncommon. We found that 48% of patients are assessed as homozygous for a GALNS alteration, 39% are assessed as heterozygous for two identified GALNS alterations, and in 13% of patients only one GALNS alteration is detected. We report here the creation of a locus-specific database for the GALNS gene (http://galns.mutdb.org/) that catalogs all reported alterations in GALNS to date. We highlight the challenges both in alteration detection and genotype-phenotype interpretation caused in part by the heterogeneity of GALNS alterations and provide recommendations for molecular testing of GALNS.

Reliable method for calculating the center of rotation in parallel-beam tomography.

High-throughput processing of parallel-beam X-ray tomography at synchrotron facilities is lacking a reliable and robust method to determine the center of rotation in an automated fashion, i.e. without the need for a human scorer. Well-known techniques based on center of mass calculation, image registration, or reconstruction evaluation work well under favourable conditions but they fail in cases where samples are larger than field of view, when the projections show low signal-to-noise, or when optical defects dominate the contrast. Here we propose an alternative technique which is based on the Fourier analysis of the sinogram. Our technique shows excellent performance particularly on challenging data.

Direct observation of degassing during decompression of basaltic magma.

Transitions in eruptive style during volcanic eruptions strongly depend on how easily gas and magma decouple during ascent. Stronger gas-melt coupling favors highly explosive eruptions, whereas weaker coupling promotes lava fountaining and lava flows. The mechanisms producing these transitions are still poorly understood because of a lack of direct observations of bubble dynamics under natural magmatic conditions. Here, we combine x-ray radiography with a novel high-pressure/high-temperature apparatus to observe and quantify in real-time bubble growth and coalescence in basaltic magmas from 100 megapascals to surface. For low-viscosity magmas, bubbles coalesce and recover a spherical shape within 3 seconds, implying that, for lava fountaining activity, gas and melt remain coupled during the ascent up to the last hundred meters of the conduit. For higher-viscosity magmas, recovery times become longer, promoting connected bubble pathways. This apparatus opens frontiers in unraveling magmatic/volcanic processes, leading to improved hazard assessment and risk mitigation.

A well-preserved 'placoderm' (stem-group Gnathostomata) upper jaw from the Early Devonian of Mongolia clarifies jaw evolution.

The origin of jaws and teeth remains contentious in vertebrate evolution. 'Placoderms' (Silurian-Devonian armoured jawed fishes) are central to debates on the origins of these anatomical structures. 'Acanthothoracids' are generally considered the most primitive 'placoderms'. However, they are so far known mainly from disarticulated skeletal elements that are typically incomplete. The structure of the jaws-particularly the jaw hinge-is poorly known, leaving open questions about their jaw function and comparison with other placoderms and modern gnathostomes. Here we describe a near-complete 'acanthothoracid' upper jaw, allowing us to reconstruct the likely orientation and angle of the bite and compare its morphology with that of other known 'placoderm' groups. We clarify that the bite position is located on the upper jaw cartilage rather than on the dermal cheek and thus show that there is a highly conserved bite morphology among most groups of 'placoderms', regardless of their overall cranial geometry. Incorporation of the dermal skeleton appears to provide a sound biomechanical basis for jaw origins. It appears that 'acanthothoracid' dentitions were fundamentally similar in location to that of arthrodire 'placoderms', rather than resembling bony fishes. Irrespective of current phylogenetic uncertainty, the new data here resolve the likely general condition for 'placoderms' as a whole, and as such, ancestral morphology of known jawed vertebrates.

On Acquisition Parameters and Processing Techniques for Interparticle Contact Detection in Granular Packings Using Synchrotron Computed Tomography.

X-ray computed tomography (XCT) is regularly employed in geomechanics to non-destructively measure the solid and pore fractions of soil and rock from reconstructed 3D images. With the increasing availability of high-resolution XCT imaging systems, researchers now seek to measure microfabric parameters such as the number and area of interparticle contacts, which can then be used to inform soil behaviour modelling techniques. However, recent research has evidenced that conventional image processing methods consistently overestimate the number and area of interparticle contacts, mainly due to acquisition-driven image artefacts. The present study seeks to address this issue by systematically assessing the role of XCT acquisition parameters in the accurate detection of interparticle contacts. To this end, synchrotron XCT has been applied to a hexagonal close-packed arrangement of glass pellets with and without a prescribed separation between lattice layers. Different values for the number of projections, exposure time, and rotation range have been evaluated. Conventional global grey value thresholding and novel U-Net segmentation methods have been assessed, followed by local refinements at the presumptive contacts, as per recently proposed contact detection routines. The effect of the different acquisition set-ups and segmentation techniques on contact detection performance is presented and discussed, and optimised workflows are proposed.

Quantification of Interdependent Dynamics during Laser Additive Manufacturing Using X-Ray Imaging Informed Multi-Physics and Multiphase Simulation.

Laser powder bed fusion (LPBF) can produce high-value metallic components for many industries; however, its adoption for safety-critical applications is hampered by the presence of imperfections. The interdependency between imperfections and processing parameters remains unclear. Here, the evolution of porosity and humps during LPBF using X-ray and electron imaging, and a high-fidelity multiphase process simulation, is quantified. The pore and keyhole formation mechanisms are driven by the mixing of high temperatures and high metal vapor concentrations in the keyhole is revealed. The irregular pores are formed via keyhole collapse, pore coalescence, and then pore entrapment by the solidification front. The mixing of the fast-moving vapor plume and molten pool induces a Kelvin-Helmholtz instability at the melt track surface, forming humps. X-ray imaging and a high-fidelity model are used to quantify the pore evolution kinetics, pore size distribution, waviness, surface roughness, and melt volume under single layer conditions. This work provides insights on key criteria that govern the formation of imperfections in LPBF and suggest ways to improve process reliability.

Dendritic crystallization in hydrous basaltic magmas controls magma mobility within the Earth's crust.

The majority of basaltic magmas stall in the Earth's crust as a result of the rheological evolution caused by crystallization during transport. However, the relationships between crystallinity, rheology and eruptibility remain uncertain because it is difficult to observe dynamic magma crystallization in real time. Here, we present in-situ 4D data for crystal growth kinetics and the textural evolution of pyroxene during crystallization of trachybasaltic magmas in high-temperature experiments under water-saturated conditions at crustal pressures. We observe dendritic growth of pyroxene on initially euhedral cores, and a surprisingly rapid increase in crystal fraction and aspect ratio at undercooling ≥30 °C. Rapid dendritic crystallization favours a rheological transition from Newtonian to non-Newtonian behaviour within minutes. We use a numerical model to quantify the impact of rapid dendritic crystallization on basaltic dike propagation, and demonstrate its dramatic effect on magma mobility and eruptibility. Our results provide insights into the processes that control whether intrusions lead to eruption or not.

Preliminary paleohistological observations of the StW 573 ('Little Foot') skull.

Numerous aspects of early hominin biology remain debated or simply unknown. However, recent developments in high-resolution imaging techniques have opened new avenues in the field of paleoanthropology. More specifically, X-ray synchrotron-based analytical imaging techniques have the potential to provide crucial details on the ontogeny, physiology, biomechanics, and biological identity of fossil specimens. Here we present preliminary results of our X-ray synchrotron-based investigation of the skull of the 3.67-million-year-old Australopithecus specimen StW 573 ('Little Foot') at the I12 beamline of the Diamond Light Source (United Kingdom). Besides showing fine details of the enamel (i.e., hypoplasias) and cementum (i.e., incremental lines), as well as of the cranial bone microarchitecture (e.g., diploic channels), our synchrotron-based investigation reveals for the first time the 3D spatial organization of the Haversian systems in the mandibular symphysis of an early hominin.

Quantitation of microcomputed tomography-imaged ocular microvasculature.

PURPOSE: To quantitatively assess microvascular dimensions in the eyes of neonatal wild-type and VEGF(120)-tg mice, using a novel combination of techniques which permit three-dimensional (3D) image reconstruction. METHODS: A novel combination of techniques was developed for the accurate 3D imaging of the microvasculature and demonstrated on the hyaloid vasculature of the neonatal mouse eye. Vascular corrosion casting is used to create a stable replica of the vascular network and X-ray microcomputed tomography (muCT) to obtain the 3D images. In-house computer-aided image analysis techniques were then used to perform a quantitative morphological analysis of the images. RESULTS: With the use of these methods, differences in the numbers of vessel segments, their diameter, and volume of vessels in the vitreous compartment were quantitated in wild-type neonatal mice or littermates over-expressing a labile (nonheparin binding) isoform of vascular endothelial growth factor (VEGF(120)) from the developing lens. This methodology was instructive in demonstrating that hyaloid vascular networks in VEGFA(120) over-expressing mice have a 10-fold increase in blind-ended, a six-fold increase in connected vessel segments, in addition to a sixfold increase (0.0314 versus 0.0051 mm(3)) in total vitreous vessel volume compared with wild type. These parameters are not readily quantified via histological, ultrastructural, or stereological analysis. CONCLUSION: The combination of techniques described here provides the first 3D quantitative characterization of vasculature in an organ system; i.e., the neonatal murine intra-ocular vasculature in both wild-type mice and a transgenic model of lens-specific over-expression of VEGF.

High-energy, high-resolution, fly-scan X-ray phase tomography.

High energy X-ray phase contrast tomography is tremendously beneficial to the study of thick and dense materials with poor attenuation contrast. Recently, the X-ray speckle-based imaging technique has attracted widespread interest because multimodal contrast images can now be retrieved simultaneously using an inexpensive wavefront modulator and a less stringent experimental setup. However, it is time-consuming to perform high resolution phase tomography with the conventional step-scan mode because the accumulated time overhead severely limits the speed of data acquisition for each projection. Although phase information can be extracted from a single speckle image, the spatial resolution is deteriorated due to the use of a large correlation window to track the speckle displacement. Here we report a fast data acquisition strategy utilising a fly-scan mode for near field X-ray speckle-based phase tomography. Compared to the existing step-scan scheme, the data acquisition time can be significantly reduced by more than one order of magnitude without compromising spatial resolution. Furthermore, we have extended the proposed speckle-based fly-scan phase tomography into the previously challenging high X-ray energy region (120 keV). This development opens up opportunities for a wide range of applications where exposure time and radiation dose are critical.

Physics of animal health: on the mechano-biology of hoof growth and form.

Global inequalities in economic access and agriculture productivity imply that a large number of developing countries rely on working equids for transport/agriculture/mining. Therefore, the understanding of hoof conditions/shape variations affecting equids' ability to work is still a persistent concern. To bridge this gap, using a multi-scale interdisciplinary approach, we provide a bio-physical model predicting the shape of equids' hooves as a function of physical and biological parameters. In particular, we show (i) where the hoof growth stress originates from, (ii) why the hoof growth rate is one order of magnitude higher than the proliferation rate of epithelial cells and (iii) how the soft-to-hard transformation of the epithelium is possible allowing the hoof to fulfil its function as a weight-bearing element. Finally (iv), we demonstrate that the reason for hoof misshaping is linked to the asymmetrical design of equids' feet (shorter quarters/long toe) together with the inability of the biological growth stress to compensate for such an asymmetry. Consequently, the hoof can adopt a dorsal curvature and become 'dished' overtime, which is a function of the animal's mass and the hoof growth rate. This approach allows us to discuss the potential occurrence of this multifaceted pathology in equids.

In situ X-ray imaging of defect and molten pool dynamics in laser additive manufacturing.

The laser-matter interaction and solidification phenomena associated with laser additive manufacturing (LAM) remain unclear, slowing its process development and optimisation. Here, through in situ and operando high-speed synchrotron X-ray imaging, we reveal the underlying physical phenomena during the deposition of the first and second layer melt tracks. We show that the laser-induced gas/vapour jet promotes the formation of melt tracks and denuded zones via spattering (at a velocity of 1 m s-1). We also uncover mechanisms of pore migration by Marangoni-driven flow (recirculating at a velocity of 0.4 m s-1), pore dissolution and dispersion by laser re-melting. We develop a mechanism map for predicting the evolution of melt features, changes in melt track morphology from a continuous hemi-cylindrical track to disconnected beads with decreasing linear energy density and improved molten pool wetting with increasing laser power. Our results clarify aspects of the physics behind LAM, which are critical for its development.